A phylogeny of the Platyhelminthes: towards a total-evidence solution

We advocate a total-evidence approach for the reconstruction of working phylogenies for the Turbellaria and the phylum Platyhelminthes. Few morphology-based character matrices are available in the systematic literature concerning flatworms, and molecular-based phylogenies are rapidly providing the only means by which we can estimate phylogenies cladistically. Character matrices based on gross morphology and ultrastructure are required and should be internally consistent, i.e. character coding should follow a set of a priori guidelines and character duplication and contradiction is avoided. In order to test our molecular phylogenies we need complementary data sets from morphology. To understand morphological homology we need phylogenetic evidence from independent (e.g. molecular) data. Fully complementary morphological and molecular data sets enable us to validate phylogenetic hypotheses and the combination of these sets in phylogenetic reconstruction utilises all statements of homology. Working phylogenies which include all phylogenetic information not only shed light on individual character evolution, but form a strong basis for comparative studies investigating the origin and evolutionary radiation of the taxonomic group under scrutiny. This revised version was published online in July 2006 with corrections to the Cover Date.     

New journal: Algorithms for Molecular Biology

This editorial announces Algorithms for Molecular Biology, a new online open access journal published by BioMed Central. By launching the first open access journal on algorithmic bioinformatics, we provide a forum for fast publication of high-quality research articles in this rapidly evolving field. Our journal will publish thoroughly peer-reviewed papers without length limitations covering all aspects of algorithmic data analysis in computatioal biology. Publications in Algorithms for Molecular Biology are easy to find, highly visible and tracked by organisations such as PubMed. An established online submission system makes a fast reviewing procedure possible and enables us to publish accepted papers without delay. All articles published in our journal are permanently archived by PubMed Central and other scientific archives. We are looking forward to receiving your contributions.     

Open by default: a proposed copyright license and waiver agreement for open access research and data in peer-reviewed journals

ABSTRACT: Copyright and licensing of scientific data, internationally, are complex and present legal barriers to data sharing, integration and reuse, and therefore restrict the most efficient transfer and discovery of scientific knowledge. Much data are included within scientific journal articles, their published tables, additional files (supplementary material) and reference lists. However, these data are usually published under licenses which are not appropriate for data. Creative Commons CC0 is an appropriate and increasingly accepted method for dedicating data to the public domain, to enable data reuse with the minimum of restrictions. BioMed Central is committed to working towards implementation of open data-compliant licensing in its publications. Here we detail a protocol for implementing a combined Creative Commons Attribution license (for copyrightable material) and Creative Commons CC0 waiver (for data) agreement for content published in peer-reviewed open access journals. We explain the differences between legal requirements for attribution in copyright, and cultural requirements in scholarship for giving individuals credit for their work through citation. We argue that publishing data in scientific journals under CC0 will have numerous benefits for individuals and society, and yet will have minimal implications for authors and minimal impact on current publishing and research workflows. We provide practical examples and definitions of data types, such as XML and tabular data, and specific secondary use cases for published data, including text mining, reproducible research, and open bibliography. We believe this proposed change to the current copyright and licensing structure in science publishing will help clarify what users -- people and machines -- of the published literature can do, legally, with journal articles and make research using the published literature more efficient. We further believe this model could be adopted across multiple publishers, and invite comment on this article from all stakeholders in scientific research.     

Does phylogeny matter? Assessing the impact of phylogenetic information in ecological meta‐analysis

Meta-analysis is increasingly used in ecology and evolutionary biology. Yet, in these fields this technique has an important limitation: phylogenetic non-independence exists among taxa, violating the statistical assumptions underlying traditional meta-analytic models. Recently, meta-analytical techniques incorporating phylogenetic information have been developed to address this issue. However, no syntheses have evaluated how often including phylogenetic information changes meta-analytic results. To address this gap, we built phylogenies for and re-analysed 30 published meta-analyses, comparing results for traditional vs. phylogenetic approaches and assessing which characteristics of phylogenies best explained changes in meta-analytic results and relative model fit. Accounting for phylogeny significantly changed estimates of the overall pooled effect size in 47% of datasets for fixed-effects analyses and 7% of datasets for random-effects analyses. Accounting for phylogeny also changed whether those effect sizes were significantly different from zero in 23 and 40% of our datasets (for fixed- and random-effects models, respectively). Across datasets, decreases in pooled effect size magnitudes after incorporating phylogenetic information were associated with larger phylogenies and those with stronger phylogenetic signal. We conclude that incorporating phylogenetic information in ecological meta-analyses is important, and we provide practical recommendations for doing so.     

Modeling body size evolution in Felidae under alternative phylogenetic hypotheses

The use of phylogenetic comparative methods in ecological research has advanced during the last twenty years, mainly due to accurate phylogenetic reconstructions based on molecular data and computational and statistical advances. We used phylogenetic correlograms and phylogenetic eigenvector regression (PVR) to model body size evolution in 35 worldwide Felidae (Mammalia, Carnivora) species using two alternative phylogenies and published body size data. The purpose was not to contrast the phylogenetic hypotheses but to evaluate how analyses of body size evolution patterns can be affected by the phylogeny used for comparative analyses (CA). Both phylogenies produced a strong phylogenetic pattern, with closely related species having similar body sizes and the similarity decreasing with increasing distances in time. The PVR explained 65% to 67% of body size variation and all Moran's I values for the PVR residuals were non-significant, indicating that both these models explained phylogenetic structures in trait variation. Even though our results did not suggest that any phylogeny can be used for CA with the same power, or that "good" phylogenies are unnecessary for the correct interpretation of the evolutionary dynamics of ecological, biogeographical, physiological or behavioral patterns, it does suggest that developments in CA can, and indeed should, proceed without waiting for perfect and fully resolved phylogenies.     

Withdrawal: Booher,Adam & Kathryn Oths. The last bonesetter: An encounter with Don Felipe. DVD/PAL, 27 mins,colour. Watertown,Mass: DER, 2018. $295.00 (institutional use). Reviewed by Howard Reid

The above article from Journal of the Royal Anthropological Institute, published online on 5 December 2022, in Wiley Online Library ( wileyonlinelibrary.com ), has been withdrawn by agreement between the journal Editors in Chief, Hannah Knox, Adam Reed, Chika Watanabe, and Thomas Yarrow, and John Wiley & Sons Ltd. The withdrawal has been agreed due to a technical error at the publisher that caused the article to be mistakenly published online although its author has not signed the journal's publishing license.     

HTLV-1 p30II: selective repressor of gene expression

Retrovirology has been publishing as an Open Access online journal for approximately six months. In this editorial, I review the reasons for and the advantages of Open Access publishing, update our progress to date, and summarize where we intend to go with this journal.     

Withdrawn: X. Chen,Y. Li,M. Zhang,X. Wu,J. Zhu. Silencing LCK inactivates the NF-κB pathway to attenuate cartilage injury in osteoarthritis: An in vivo and in vitro study,published in The Journal of Gene Medicine.

The above article, published online on 10 August 2021 in Wiley Online Library ( wileyonlinelibrary.com ), has been withdrawn by agreement between the journal Editor in Chief, Gening Jiang, and John Wiley & Sons Ltd. The withdrawal has been agreed following no response from the author to requests to sign the Journal's publishing license.     

Withdrawn: Z. Cui,Q. Sun,W. Yan,Q. Han,G. Wang,Y. Hu. The role of miR-320a and its target gene GMEB1 in epithelial-mesenchymal transition and invasion of colorectal cancer,published in The Journal of Gene Medicine.

The above article, published online on 22 February 2021 in Wiley Online Library ( wileyonlinelibrary.com ), has been withdrawn by agreement between the journal Editor in Chief, Gening Jiang, and John Wiley & Sons Ltd. The withdrawal has been agreed following no response from the author to requests to sign the Journal's publishing license.     

Withdrawn: L. Xuan,Z. Sun,J. Wang,S. Gao. Long non-coding RNA SNHG8 promotes ovarian cancer progression through serving as a sponge for miR-1270 to regulate S100A11 expression,published in The Journal of Gene Medicine.

The above article, published online on 25 January 2021 in Wiley Online Library (wileyonlinelibrary.com), has been withdrawn by agreement between the journal Editor in Chief, Gening Jiang, and John Wiley & Sons Ltd. The withdrawal has been agreed following no response from the author to requests to sign the Journal's publishing license.     

Withdrawn: F. Jin,M. Li,X. Li,Y. Zheng,K. Zhang,X Liu,B. Cai,G. Yin. PlncRNA-1 stimulates hair follicle stem cell differentiation in wound healing via the EZH2/ZEB1/MAPK1 axis,published in The Journal of Gene Medicine, 10.1002/jgm.3408

The above article, published online on 05 January 2022 in Wiley Online Library ( wileyonlinelibrary.com ), has been withdrawn by agreement between the journal Editor in Chief, Gening Jiang, and John Wiley & Sons Ltd. The withdrawal has been agreed following no response from the author to requests to sign the Journal's publishing license.     

Effectiveness of journal ranking schemes as a tool for locating information

Background

The rise of electronic publishing [1], preprint archives, blogs, and wikis is raising concerns among publishers, editors, and scientists about the present day relevance of academic journals and traditional peer review [2]. These concerns are especially fuelled by the ability of search engines to automatically identify and sort information [1]. It appears that academic journals can only remain relevant if acceptance of research for publication within a journal allows readers to infer immediate, reliable information on the value of that research.

Methodology/Principal Findings

Here, we systematically evaluate the effectiveness of journals, through the work of editors and reviewers, at evaluating unpublished research. We find that the distribution of the number of citations to a paper published in a given journal in a specific year converges to a steady state after a journal-specific transient time, and demonstrate that in the steady state the logarithm of the number of citations has a journal-specific typical value. We then develop a model for the asymptotic number of citations accrued by papers published in a journal that closely matches the data.

Conclusions/Significance

Our model enables us to quantify both the typical impact and the range of impacts of papers published in a journal. Finally, we propose a journal-ranking scheme that maximizes the efficiency of locating high impact research.     

Impact of methodological choices on assessments of the reliability of fossil primate phylogenetic hypotheses

It has been argued in several recent studies that conventional craniodental characters cannot be assumed to be reliable for the purposes of reconstructing primate phylogenetic relationships and that as a consequence little confidence can be invested in published fossil primate phylogenies. Here, we evaluate this claim by revisiting the analyses reported in one of these studies [Collard and Wood, 2000]. Specifically, we investigate whether the use of alternative methodological procedures would have altered their findings. We focus on three key issues: (1) size correction, (2) outgroup composition and (3) non-phylogenetic correlation among characters. Our analyses suggest that the results of Collard and Wood [2000] were not affected by the size correction method they used or by the outgroup they employed. Our analyses also suggest that their results were not affected by their decision to ignore developmental, functional and other non-phylogenetic correlations among the characters in their data sets. Accordingly, our study supports the assertion that conventional craniodental characters cannot be assumed to be reliable for reconstructing primate phylogenetic relationships. This in turn suggests that many published fossil primate phylogenies may be unreliable.     

Expression of Concern: Pari,L. and Rajarajeswari,N. (2011). Antioxidant role of coumarin on streptozotocin–nicotinamide‐induced type 2 diabetic rats. J. Biochem. Mol. Toxicol., 25: 355‐361. https://doi.org/10.1002/jbt.20395

This expression of concern is for the above article, published online on May 31, 2011, in Wiley Online Library ( wileyonlinelibrary.com ), and has been published by agreement between the journal Editor‐in‐Chief, Dr Hari K. Bhat, and Wiley Periodicals, LLC. This expression of concern has been issued following concerns raised regarding the appearance of Figure 4A and the narrow range of standard deviations presented in Tables 1 and 2. The authors and the authors' institution failed to respond to a request from the Publisher and the Editor‐in‐Chief to investigate whether the images and data arose from the originally reported experiments, are unmodified, and are suitable for publication. As a result, the journal is issuing this expression of concern to readers.     

Retraction

These articles have been retracted at the request of the authors.Reason: In July of 2002, Mechanisms of Development started publishing its section Gene Expression Patterns (until then included under the Mechanisms of Development title) under the separate title Gene Expression Patterns, as a separate section of Mechanisms of Development.This change was clearly communicated at the time in the journal and on the journal’s web site. The Editors also informed the authors about this. Early 2003, it came to our attention that a mistake was made during the split with regard to a number of Gene Expression Patterns articles in the pipeline (between initial submission and final acceptance). Due to a miscommunication for which the publisher accepts the responsibility, not all the editors used the same cut-off date for the split. As a result, some articles have been published under the Gene Expression Patterns title that should have been published in the main section of Mechanisms of Development. The publisher is very much aware of the serious nature of this mistake and we apologise to the authors, readers and editors of the journal.In the first months of 2003, we consulted with a number of the authors involved to discuss possible options to remedy the situation, and at the request of the authors, we agreed to retract the articles of the authors concerned, who requested this. We also agreed to offer this opportunity to those authors who were notified by the editors, but who misunderstood the message due to the fact that the proofs of their article still had the MoD logo and title on the opening page. The articles are re-published in supplement 1 to Vol. 119 under the Mechanisms of Development title.The Publisher     

Toward a standards-compliant genomic and metagenomic publication record

Increasingly, we are aware as a community of the growing need to manage the avalanche of genomic and metagenomic data, in addition to related data types like ribosomal RNA and barcode sequences, in a way that tightly integrates contextual data with traditional literature in a machine-readable way. It is for this reason that the Genomic Standards Consortium (GSC) formed in 2005. Here we suggest that we move beyond the development of standards and tackle standards compliance and improved data capture at the level of the scientific publication. We are supported in this goal by the fact that the scientific community is in the midst of a publishing revolution. This revolution is marked by a growing shift away from a traditional dichotomy between "journal articles" and "database entries" and an increasing adoption of hybrid models of collecting and disseminating scientific information. With respect to genomes and metagenomes and related data types, we feel the scientific community would be best served by the immediate launch of a central repository of short, highly structured "Genome Notes" that must be standards compliant. This could be done in the context of an existing journal, but we also suggest the more radical solution of launching a new journal. Such a journal could be designed to cater to a wide range of standards-related content types that are not currently centralized in the published literature. It could also support the demand for centralizing aspects of the "gray literature" (documents developed by institutions or communities) such as the call by the GSC for a central repository of Standard Operating Procedures describing the genomic annotation pipelines of the major sequencing centers. We argue that such an "eJournal," published under the Open Access paradigm by the GSC, could be an attractive publishing forum for a broader range of standardization initiatives within, and beyond, the GSC and thereby fill an unoccupied yet increasingly important niche within the current research landscape.     

Phylogenetic diversity meets conservation policy: small areas are key to preserving eucalypt lineages

Evolutionary and genetic knowledge is increasingly being valued in conservation theory, but is rarely considered in conservation planning and policy. Here, we integrate phylogenetic diversity (PD) with spatial reserve prioritization to evaluate how well the existing reserve system in Victoria, Australia captures the evolutionary lineages of eucalypts, which dominate forest canopies across the state. Forty-three per cent of remaining native woody vegetation in Victoria is located in protected areas (mostly national parks) representing 48% of the extant PD found in the state. A modest expansion in protected areas of 5% (less than 1% of the state area) would increase protected PD by 33% over current levels. In a recent policy change, portions of the national parks were opened for development. These tourism development zones hold over half the PD found in national parks with some species and clades falling entirely outside of protected zones within the national parks. This approach of using PD in spatial prioritization could be extended to any clade or area that has spatial and phylogenetic data. Our results demonstrate the relevance of PD to regional conservation policy by highlighting that small but strategically located areas disproportionally impact the preservation of evolutionary lineages.     

Taxon sampling effects on the quantification and comparison of community phylogenetic diversity

Ecologists are increasingly making use of molecular phylogenies, especially in the fields of community ecology and conservation. However, these phylogenies are often used without full appreciation of their underlying assumptions and uncertainties. A frequent practice in ecological studies is inferring a phylogeny with molecular data from taxa only within the community of interest. These “inferred community phylogenies” are inherently biased in their taxon sampling. Despite the importance of comprehensive sampling in constructing phylogenies, the implications of using inferred community phylogenies in ecological studies have not been examined. Here, we evaluate how taxon sampling affects the quantification and comparison of community phylogenetic diversity using both simulated and empirical data sets. We demonstrate that inferred community trees greatly underestimate phylogenetic diversity and that the probability of incorrectly ranking community diversity can reach up to 25%, depending on the dating methods employed. We argue that to reach reliable conclusions, ecological studies must improve their taxon sampling and generate the best phylogeny possible.     

Retracted: Britannin mediates apoptosis and glycolysis of T-cell lymphoblastic lymphoma cells by AMPK-dependent autophagy

The above article, published online on 19 September 2022 in Wiley Online Library ( https://onlinelibrary.wiley.com/doi/abs/10.1002/jbt.23211 ), has been retracted by agreement between the authors, the journal Editor in Chief, Hari Bhat, and Wiley Periodicals, LLC. The article is being retracted at the authors' request because some of the data underlying this article refer to a different cell line from the one reported in it. As a result, the article's conclusions do not accurately reflect the full data and cannot be considered reliable.